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10x Single cell data analysis with Monocle

Has anyone tried using a Seurat object or 10x data in Monocle? I was trying in several ways...Disappointed to get error messages like "the object type you want to export to is not supported yet"; could not find function "load_cellranger_matrix" etc., Looks like the latest version of Monocle is not compatible with Seurat objects...??? Is there any other way around? Any thoughts or suggestions would be helpful!!! Thank you!

rna-seq
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updated by igor igor • written by vk5k • vk5k

A couple of points on your post:

  1. This is a Question-type post, not a Forum discussion. I've made the necessary change. To learn more, please read posts under the how-to tag.
  2. Please avoid informal writing quirks such as multiple punctuation marks, ellipsis to evoke a sense of time, etc. Remember, ??? is taken less seriously than ?. We are on a professional forum - not on reddit or Facebook.
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written by Ram Ram

My sincere apologies. I am very new to this forum and am not familiar with the rules to follow. Thanks for your pointers.

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written by vk5k • vk5k

1 answer

You can find code used to convert a Seurat 3 object to a Monocle 3 object here: https://github.com/cole-trapnell-lab/monocle3/issues/262

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written by igor igor

Thanks for sharing the link!

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written by vk5k • vk5k

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